New flaws in the government's national identity card scheme have emerged with the disclosure today that the microchips in 3m passports, which are supposed to be valid for 10 years, only carry a 24-month warranty.

Whitehall spending watchdogs also warn today that much of the technology surrounding the new ePassports is still unproven and could lead to passenger delays at airports, raising doubts about their immediate security benefits.

A National Audit Office report says the £440m Home Office ePassports project has so far been delivered on time and on budget but flaws in its technology mean that it may still prove not to be value for money. The cost of renewing a passport has been increased from £51 to £66 to pay for the introduction of ePassports which include a digital photograph and biographical details held on a microchip which is read by an electronic scanner at immigration control.

The government hopes that by 2012 all British passport holders will have changed to an electronic passport enabling a system which counts everybody in and out of the country to be put in place as the major component of an ID cards scheme.

The NAO report says flaws that have emerged include:

· Philips Semiconductors have only given a 24-month warranty for the microchip units, despite a 10-year lifespan for the passports. The identity and passport service which runs the scheme could face a high number of returned passports, leading to further rises in the renewal fee.

· Although 3m ePassports have already been issued, the upgrading of passport readers at UK airports will not be completed until later this year. The new readers - which take eight seconds to work - could lead to delays for travellers.

· Facial recognition technology is not reliable enough to allow automatic checking of passport applications against the full database of existing passport holders.

Whitehall's auditors also say that immigration officers will only be able to check at their front desk whether the printed passport photograph matches the electronic image held on the chip. Any other checks such as if the passport is genuine or if it has been tampered with will require them to go to the back office to scan it against the more sophisticated reader. A further 200 scanners, each costing £1,300, which can read the digital signature to check if the passport is genuine, are to be installed in back offices while the problems with the front desk readers are sorted out.

"This creates the risk that ePassport chips may not be read frequently enough to deliver the full security benefits," warns the NAO report.

Edward Leigh, chairman of the Commons public accounts committee, said: "It is most worrying that the warranty deal the IPS struck to cover the passport chips lasts only two years. We will all be hoping that ePassports don't fail, leaving us stranded at the check-in gate." The Home Office minister, Joan Ryan, said the ePassport would ensure continued visa-free travel to the US. She confirmed that the ID card scheme would build on the ePassports project: "This will include incorporating fingerprint data in passports starting in late 2009 to keep our passports amongst the most secure in the world."